title: Genome-wide analysis of genetic alterations in testicular primary seminoma using high resolution single nucleotide polymorphism arrays.
abstract: Testicular germ cell tumors (TGCT) represent the most common malignancy among young males. To our knowledge no comprehensive Copy Number Variation (CNVs) studies of TGCT using high-resolution Single Nucleotide Polymorphism (SNP) array have been performed. By a genome-wide analysis of CNV and loss of heterozygosity (LOH) in 25 primary seminomas, we confirmed several previously reported genomic alterations and discovered eight novel genomic alterations including amplifications and homozygous deletions. Moreover, a comparison of genomic alterations of early and late stage seminoma identified CNVs that correlate with progression, which included deletions in chromosomes 4q, 5p, 9q, 13q and 20p and amplifications in chromosomes 9q and 13q. We compared previously perform Affymetrix expression analysis in a subset of samples and found robust correlation between expression and genomic alterations. Furthermore, high correlations (40-75%) were observed between CNV by SNP analysis and quantitative PCR. Our findings may lead to better understanding of TGTC's pathogenesis.
authors.affiliation: Johns Hopkins University, School of Medicine, Department of Otolaryngology, Head and Neck Cancer Research, Baltimore MD, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: LeBron
authors.forename: Prodipto
authors.initials: P
authors.lastname: Pal
authors.forename: Mariana
authors.initials: M
authors.lastname: Brait
authors.forename: Santanu
authors.initials: S
authors.lastname: Dasgupta
authors.forename: Rafael
authors.initials: R
authors.lastname: Guerrero-Preston
authors.forename: Leendert H J
authors.initials: LH
authors.lastname: Looijenga
authors.forename: Jeanne
authors.initials: J
authors.lastname: Kowalski
authors.forename: George
authors.initials: G
authors.lastname: Netto
authors.forename: Mohammad O
authors.initials: MO
authors.lastname: Hoque
mesh_terms: D000328:Adult; D002877:Chromosomes, Human / Q000235:genetics; D056915:DNA Copy Number Variations; D005784:Gene Amplification; D052138:Genes, Neoplasm; D055106:Genome-Wide Association Study; D006801:Humans; D019656:Loss of Heterozygosity; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D018239:Seminoma / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D017384:Sequence Deletion; D013736:Testicular Neoplasms / Q000235:genetics*